By Izzy Lopez

When the coronavirus pandemic began in March, María Suarez, junior in bioengineering, left Penn’s campus and returned home to Costa Rica. What should have been the final weeks of club activities, social events and end-of-year celebrations shifted to months spent at home, far away from Philadelphia. But Suarez, like many others, wanted to do something productive with her time in quarantine. Drawing on her bucolic roots, she decided to start a garden.

“I was born and raised in a very rural area,” Suarez says. “There is a huge river in my backyard where I learned how to count by throwing pebbles in the river with my mother and sister. Nature is a big part of my life, and it’s really shaped my personality. As a child, I planted herbs, like basil, mint and oregano, with my parents. When you are close to the land like this, gardening was something that grew naturally out of our lifestyle.”

As the spring semester shifted into summer, Suarez returned to her love of planting and embarked on an ambitious project to grow a vegetable garden in her backyard. Unlike the smaller herb gardens she had grown as a child, this vegetable garden required deeper horticultural knowledge as well as intense work under the hot sun.

“To begin the garden, I had to clear the land I wanted to use and remove all the grass and stones from the soil,” Suarez shares. “It was the dry season in Costa Rica and the ground was very difficult to work with.”

After clearing the land, Suarez had to bring nutrients back into the soil of her garden plot. Luckily, her family has been maintaining a natural compost pile for many years.

“Basically, the compost pile is a hole in the ground where we put our natural food waste. There are worms and animals there that help us naturally decompose the waste and they produce a very nutrient rich soil.” Suarez explains. “The compost is a five-minute walk from my garden, and I had to take at least ten trips with a wheelbarrow to bring enough back. It was a great arm workout.”

Once the soil was placed and watered, Suarez was finally able to plant her seeds. After a few days, she saw celery and zucchini plants beginning to sprout. Throughout the summer, Suarez’s crops grew well, and she was able to harvest the vegetables and share them with her family.

“It was very fulfilling to see the products of my efforts,” Suarez says.

While growing her vegetable garden has reaped many rewards — such as fresh herbs and produce to share with her family — it also came with challenges. In August, Suarez noticed that her garden’s production decreased, so she consulted local farmers for advice.

“They brought to my attention that if I kept planting on the same soil, it would run out of nutrients,” says Suarez. “To solve this, I took soil from my personal compost bin and added it to my garden. I also changed the type of vegetables I was planting to allow different nutrients in the soil to regenerate.”

While Suarez is still learning the best practices for tending her garden, she has even bigger plans for her plants in the coming months. In Costa Rica, many crops fail as a result of weeds or diseases that live in the natural soil. Suarez believes that hydroponic planting — a method of growing plants in pools of water and nutrients instead of soil — could be the future of Costa Rican agriculture. She is testing her theory with her own garden. Last winter, while home on break from Penn, Suarez and her father built a small hydroponic garden using PVC pipes. Now, Suarez is scaling up to build a hydroponic greenhouse. It’s still under construction, but Suarez is excited about the project.

“I’m working on finishing the structure of the greenhouse and developing a water circulation system,” Suarez says. “Currently, my garden doesn’t have access to electricity for an automatic system. That is a big challenge, but I believe that my Penn Engineering knowledge will help me create something pretty cool.”

Suarez argues that hydroponic gardening offers the opportunity for vertical planting which would minimize land use and maximizes the efficiency of each square foot of planting.

“Costa Rica is a place that depends heavily on agriculture but, as it is now, crops die from soil-borne diseases and people depending on the crops suffer through very difficult times as a result,” she notes. Suarez hopes that her experiments in hydroponics can help others like her who are interested in growing gardens in difficult terrain.

All this time spent in the garden has given Suarez a new perspective on the meaning of hard work.

“My mother often says, ‘If you plant in fertile soil, you will get results,’” Suarez shares. “Usually, when she says this, I complain. But after growing this garden, I see what she means. Something I like about planting is that I get to see that if I put in the hard work, I am going to get good results. It’s a very tangible reward for my efforts, and that feels great.”

Throughout the summer, Suarez has been able to enjoy some of her harvest, such as cilantro, green beans and cucumbers. Like many other Penn Engineering students, Suarez will be participating in virtual classes this semester from her home in Costa Rica. While this isn’t what she anticipated for Fall 2020, Suarez says tending her garden has been an enriching experience during a difficult time.

“This garden has been a great experience so far,” Suarez shares. “I would recommend it to anyone who has the space to plant something right now. It’s so fulfilling and you learn a lot from it.”

Gardening in Costa Rica Yields Inspiration During Quarantine was originally published in Penn Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.

M. Ani Hsieh, research associate professor in the Department of Mechanical Engineering and Applied Mechanics, has been named Deputy Director of the General Robotics, Automation, Sensing and Perception (GRASP) Laboratory. Hsieh assumes the role as former Deputy Director CJ Taylor transitions to his new position, Penn Engineering’s first Associate Dean for Diversity, Equity, and Inclusion.

Hsieh, who began her tenure in the GRASP Lab as a graduate student, is an expert in the control and planning of multi-agent robotic systems. She is particularly interested in marine robotic systems and their applications in environmental monitoring.

Though the open ocean is a particularly challenging environment for anything containing delicate machinery and electronics, ocean currents and waves can help propel fleets of miniature, autonomous robots and provide data relevant to studying the spread of pollution, climate change, and more.

Hsieh’s work has been recognized by her receipt of the Office of Naval Research Young Investigator Award and the National Science Foundation CAREER Award.

Ani Hsieh Named Deputy Director of GRASP Lab was originally published in Penn Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.

Kristian Lum, Research Assistant Professor in the Department of Computer and Information Science, was recently featured on ACM ByteCast, a podcast series from the Association for Computing Machinery that covers a range of topics at the intersection of computing research and practice.

Kristian Lum - Episode 4

Host Rashmi Mohan spoke with Lum about her unique path to Penn Engineering and her prior work as the lead statistician at the Human Rights Data Analysis Group, where she used data science to uncover racial biases in the United States criminal justice system. Lum is widely known for her work on algorithmic fairness and predictive policing and is a key organizer of the ACM Conference on Fairness, Accountability, and Transparency.

Beginning in math and statistics, Lum began her career in a lab working with bioinformatics. This work expanded her interest in social issues and brought her to her positions with the Human Rights Data Analysis Group. In her conversation with Mohan, Lum discusses the importance and ethics of data privacy, especially when it applies to incarcerated peoples’ identifying information.

“When we’re talking about data from the criminal justice system,” Lum says, “we get into some ethical grey areas where some of the data we have is a matter of public record and you can find it in the world. But this brings up the question of what we should do with it. Even if it’s out there, once you have researchers using it, there are questions about how appropriate it is to publish that data with the individual’s name attached to it.”

In addition to her human rights work, Lum is currently working on new COVID-19 models that account for the time lag between infection and death. She hopes that this improved model will provide clearer information about the spread of COVID-19, given the lack of testing available in many places.

Listen to the full interview with Kristian Lum on ACM ByteCast.

Kristian Lum Discusses Computer Science and Social Justice on ACM ByteCast was originally published in Penn Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.

Yesterday, Marc Miskin, assistant professor in Penn Engineering’s Department of Electrical and Systems Engineering, published a paper in the journal Nature detailing a new kind of robot he developed with his colleagues and former advisors at Cornell.

Along with the paper, Nature published academic commentary explaining the significance of the paper, as well as a video illustrating how the researchers leveraged the well-understood technology of the semiconductor industry to make their robots’ bodies and added their own twist to form their legs. Each of those legs is a nanoscale strip of platinum that curls up when a voltage is applied; by precisely placing rigid plates to form “joints” along the strips, they can bend as if they had knees and ankles.

These microscopic robots are already taking the world by storm. Read more coverage of Miskin and his colleague’s development at New Scientist, CNet, BBC’s Science Focus Magazine, New Atlas and Inverse.

More on Marc Miskin’s Microscopic Robots was originally published in Penn Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.

Advances in robotics are often looked at through the lens of our own biology. Is a new humanoid robot’s gripper gentle enough to safely give a handshake? Can it keep its balance as well as a toddler?

Researchers from Penn Engineering and Cornell are looking through this lens at an even more fundamental level: creating robotic systems that are on the scale of biological cells.

They have created the first microscopic robots that are made with semiconductor processing and can be controlled — and made to walk — with standard electronic signals. Roughly the size of a paramecium, they provide a template for building even more complex versions that can be mass produced and may someday travel through the human body.

Marc Miskin, assistant professor in Penn Engineering’s Department of Electrical and Systems Engineering, began working on these robots while a postdoctoral researcher under Itai Cohen, professor of physics, and Paul McEuen, the John A. Newman Professor of Physical Science, both faculty in Cornell University’s College of Arts and Sciences.

The three have now led a study, published in the journal Nature, that outlines how these microscopic robots can be assembled and controlled.

“I remember looking into a microscope as a kid and being blown away by all these amazing tiny creatures,” says Miskin. “Biology works through microscopic machines. Even you are essentially a giant machine made out of tiny robots called cells.”

“Nature shows there’s no reason we can’t build something incredibly small and incredibly complex,” he says. “The question is how can we do it? How can humans build systems that duplicate what biological cells are doing, even in some small way?”

The researchers’ new robots are too small to be seen by eye: about 5 microns thick, 40 microns wide and ranging from 40 to 70 microns in length. Each consists of a simple circuit made from silicon photovoltaics — essentially the torso and brain — and four electrochemical actuators that function as legs.

“In the context of the robot’s brains, there’s a sense in which we’re just taking existing semiconductor technology and making it small and releasable, but the legs did not exist before,” says McEuen. “There were not small, electrically activatable actuators that you could use. So we had to invent those and then combine them with the electronics.”

Using lithography techniques similar to those employed in making computer chips, the robots’ brains and torso are etched onto silicon; roughly a million of them can fit onto a standard four-inch silicon wafer. Atomic layer deposition then adds the legs, which consist of strips of platinum, only a few dozen atoms thick. Applying a voltage causes the platinum to curl up, so rigid panels are also added on top of those strips, essentially creating joints that determine how the strips will bend when actuated.

The researchers control the robots by flashing laser pulses at different photovoltaics, each of which activates a separate set of legs. By toggling the laser back and forth, the robot walks.

The robots can currently be coaxed into skittering at a top speed of 30 microns per second, still quite slow, but the researchers believe their gaits can be optimized to emulate the more efficient motion of biological microorganisms.

“While these robots are primitive in their function — they’re not very fast, they don’t have a lot of computational capability — every single one of the innovations that we made in creating them blows open the door to making these things smart, fast and mass-producible,” Cohen says. “This is really just the first shot across the bow that, hey, we can do electronic integration on a tiny robot.”

As the researchers imbue their microscopic robots with more abilities, they envision them having applications in biological contexts, such sitting on leaves to fight agricultural pests, or circulating in the bloodstream to sense infections or cancerous cells.

“Computers changed the world by getting better, cheaper and smaller,” Miskin says. “It’s going to be really exciting to see what happens when we can start to do the same thing with robotics.”

The research was supported by the Army Research Office; the Air Force Office of Scientific Research; the Cornell Center for Materials Research, which is supported by the National Science Foundation’s Materials Research Science and Engineering Center program; and the Kavli Institute at Cornell for Nanoscale Science. The work was performed at the Cornell NanoScale Science and Technology Facility.

Penn Engineering and Cornell Researchers Develop Laser-controlled, Cell-sized Robots was originally published in Penn Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.

More than 30 inherited disorders are caused by the unstable expansion of repetitive DNA sequences, including Huntington’s disease, ALS, Fragile X syndrome, and Friedreich’s ataxia. Jennifer E. Phillips-Cremins, associate professor in Penn Engineering’s Department of Bioengineering and in the Perelman School of Medicine’s Department of Genetics, has shown another link between these disorders: the location of these expanding genes relative to the complicated folding patterns the genome exhibits to fit inside the nucleus of a cell.

Now, Phillips-Cremins is among 60 researchers taking part in a $4.5 Million Chan Zuckerberg Initiative project that aims to apply novel, interdisciplinary approaches toward investigating neurodegenerative disorders. The CZI Collaborative Pairs Pilot Project will fund 30 teams that combine clinical and basic science expertise and have at least one early- or mid-career researcher.

“We are excited to welcome the Collaborative Pairs grantees to CZI’s Neurodegeneration Challenge Network and are hopeful that the discoveries these researchers make help us understand these devastating disorders,” said CZI Head of Science, Cori Bargmann. “With this collaborative network, we’re also thrilled to support early- and mid-career scientists who bring new approaches and insights to the neurodegeneration field.”

Phillips-Cremins will collaborate with Kristen Brennand of the Icahn School of Medicine at Mount Sinai. Their project, “3D genome misfolding due to repeat instability in neurodegenerative disease,” project will investigate the emerging link between the genetic sequence’s higher-order folding patterns and pathologic repeat instability in trinucleotide repeat (TNR) expansion disorders.

In a 2018 study published in the journal Cell, Phillips-Cremins and her colleagues established a strong correlation between 3D genome misfolding, short tandem repeat instability, and pathologic gene disruption in TNR disorders, suggesting new research questions whose answers could improve diagnosis or treatment.

Jennifer Phillips-Cremins Wins CZI Grant to Study 3D Genome’s Role in Neurodegenerative Disease was originally published in Penn Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.

The School of Engineering and Applied Science’s PRECISE Center and the School of Nursing at the University of Pennsylvania have formed a partnership with medical device leader Hillrom to develop technical solutions for health care challenges in multiple domains, including critical care, diabetes, mental health, and cardiology.

This collaboration will accelerate the adoption of new technologies by clinicians via unobtrusive, frictionless sensors that respect the natural workflow of caregivers.

PRECISE’s research on the internet-of-things and medical cyber-physical systems aims to provide verifiably safe healthcare solutions that leverage data, machine learning, and formal analysis. These solutions will establish the foundations for safe, autonomous medical systems that integrate medical devices, patients, clinicians, and personalized automation to improve health outcomes.

“By closely collaborating with industry partners, such as Hillrom, we hope to transition our technologies and solutions into mainstream clinical care to revolutionize health care in the future,” says PRECISE Center Director Insup Lee, Cecilia Fitler Moore Professor in Penn Engineering’s departments of Computer and Information Science and Electrical and Systems Engineering.

“PRECISE researchers are at the forefront of ensuring that modern technologies’ embedded systems are safe and secure,” said Vijay Kumar, Nemirovsky Family Dean of Penn Engineering. “Working directly with partners in the health care industry is crucial for enabling their expertise to benefit as many people as possible.”

PRECISE, or Penn Research In Embedded Computing and Integrated Systems Engineering, is focused on the idea of “Safe AI.” Electronic systems are increasingly networked and tasked with making autonomous decisions based on the information gleaned from those networks. Those decisions can have life-or-death consequences, especially in medical settings; Safe AI is about ensuring that those systems are fundamentally reliable.

Collaborating with Penn Nursing and Hillrom will allow PRECISE researchers to better understand the unique challenges of medical settings. Beyond helping to define the scope of problems that can be handled autonomously, Safe AI research can show how to best to present critical information for problems that require a human touch.

“This is a unique opportunity to redesign the future of clinical care by fostering interdisciplinary collaboration and generating patient and family centered solutions,” says George Demiris, a Penn Integrates Knowledge University Professor with appointments in Penn Nursing and Penn’s Perelman School of Medicine.

The partnership with PRECISE and the School of Nursing accelerates Hillrom’s plan to consolidate data collected from the EMR, various Hillrom devices and new sensors, including those from Penn, to provide actionable, clinical information at the point of care.

Critically, the gathering and synthesis of this information is poised to be a powerful tool in protecting patients against “never-events” — a class of particularly egregious medical errors, such as mismatching blood types.

“Through this partnership, we will demonstrate that Hillrom smart beds, vital signs devices and other Hillrom products can be platforms for advanced sensing and algorithm development to help prevent never-events in hospitals,” says John Groetelaars, president and CEO, Hillrom. “We appreciate the opportunity to collaborate with PRECISE and look forward to helping strengthen our industry’s AI capabilities.”

“We are thrilled to be partners in this exciting new venture. The inclusion of Penn Nursing ensures important perspectives at the point of care that can best improve patient outcomes,” says Penn Nursing Dean Antonia Villarruel.

This new partnership will combine the full, interdisciplinary strength of an institution like Penn with advanced engineering and deep insights from Hillrom’s clinical and innovation experts. That triumvirate of clinical, business, and engineering disciplines on one campus is a major strength of Penn via the PRECISE Center, as it breaks down silos and fosters effective and efficient interdisciplinary collaboration with industry.

Penn Engineering and Nursing Partner with Medical Device Provider Hillrom on Internet-of-Things… was originally published in Penn Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.

Early attempts to understand how the brain works included the pseudoscience of phrenology, which theorized that various mental functions could be determined through the shape of the skull. While those theories have long been debunked, modern neuroscience has shown a kernel of truth to them: those functions are highly localized to different regions of the brain.

Now, Danielle Bassett, J. Peter Skirkanich Professor of Bioengineering and Electrical and Systems Engineering, is pioneering a new subfield that goes even deeper into the connection between the brain’s form and function: network neuroscience.

In a recent feature article in Wired, Bassett explains the concepts behind this new subfield. While prior understanding has long relied on the idea that certain areas of the brain control certain functions, Bassett and other network neuroscientists are using advances in imaging and machine learning to reveal the role the connections between those areas play.

For Bassett, one of the first indicators that these connections mattered more than previously realized was the shape of the neurons themselves.

Speaking with Wired’s Grace Huckins, Bassett says:

“Neurons are not spherical — neurons have a cell body, and then they have this long tail that allows them to connect to many other cells. You can even look at the morphology of the neuron and say, ‘Oh, well, connectivity has to matter. Otherwise, it wouldn’t look like this.’”

Read more about Bassett and the field of network neuroscience in Wired.

Danielle Bassett on ‘A Radical New Model of the Brain’ was originally published in Penn Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.

Last week, the National Science Foundation announced the Penn-headquartered IoT4Ag (Internet of Things for Precision Agriculture) Center. As one of the NSF’s Engineering Research Centers, IoT4Ag researchers will not only work on interconnected technologies designed to address food, water and energy challenges, but also forge connections between experts in a variety of fields, members of the agriculture industry, and the next generation of researchers that will take up this charge.

Cherie Kagan, Stephen J. Angello Professor in Penn Engineering’s departments of Electrical and Systems Engineering and Materials Science and Engineering, is the IoT4Ag Center’s director and principal investigator. She recently recorded a “Scientist Selfie” for the NSF, giving prospective STEM students a tour of her lab and some insight into how researchers like her tackle large-scale societal challenges.

Watch her video at NSF’s Facebook page.

Cherie Kagan, Director of New NSF Center on Agriculture Internet of Things, Takes a ‘Scientist… was originally published in Penn Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.

Danielle Bassett, J. Peter Skirkanich Professor in the departments of Bioengineering and Electrical and Systems Engineering, has been called the “doyenne of network neuroscience.” The burgeoning field applies insights from the field of network science, which studies how the structure of networks relate to their performance, to the billions of neuronal connections that make up the brain.

Much of Basset’s research draws on mathematical and engineering principles to better understand how mental traits arise, but also applies them more broadly to other challenges in neuroscience.

In her latest paper, “Defining and predicting transdiagnostic categories of neurodegenerative disease,” published in the journal Nature Biomedical Engineering, Bassett collaborated with the Perelman School of Medicine’s Virginia Man-Yee Lee and John Trojanowski to provide a new perspective on the misfolded proteins associated with those diseases.

The researchers used machine learning techniques to create a new classification system for neurodegenerative diseases, one which may redraw the boundaries between them and help explain clinical differences in patients who received the same diagnoses.

BioWorld’s Anette Breindl spoke with Bassett about the team’s findings.

Now, investigators have developed a new approach to classifying neurodegenerative disorders that used the overall patterns of protein aggregation, rather than specific proteins, to define six clusters of patients that crossed traditional diagnostic categories.

“We find that perhaps the way that clinicians have been diagnosing these disorders… is not necessarily the way these disorders work,” Danielle Bassett told BioWorld. “The way we’ve been trying to carve nature at joints is not the way that nature has joints. The joints are elsewhere.”

Continue reading Breindl’s article, “For neurodegeneration, a different way to slice the pie,” at BioWorld.

‘For Neurodegeneration, a Different Way to Slice the Pie’ was originally published in Penn Engineering on Medium, where people are continuing the conversation by highlighting and responding to this story.